EDIT: I did some thinking about things and realized I hadn't gotten Emi's Bad Ending. I kept trying different things, but for a while nothing worked, until I tried choices I hadn't made before.

It seems despite the 100% there are still things that one can miss that aren't "Labeled" so to speak, in the library. Seems like something about getting Emi's Bad Ending is one of em, maybe due to no scenes of any sort.